TEK p.Asn138=
c.414C>T · rs143058954 · VCV736779
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0254%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -2, phastCons 0.68 |
| Overall | ||
| CADD | 8.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0254%
African / African-American · 19/74,898 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.00434%
70/1,613,788 alleles · ultra-rare
exomes 56/1,461,648 · genomes 14/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0254% | 3,942 |
| Middle Eastern | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,410 |
| European (non-Finnish) | 0.00347% | 28,778 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| East Asian | 0.00223% | 44,858 |
| Admixed American | 0.00167% | 59,988 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TEK
- Protein
- p.Asn138=
- Coding
- c.414C>T
- MANE Select
- NM_000459
- dbSNP
- rs143058954
- Type
- single nucleotide variant
- Location
- chr9:27168544 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 17 PDB
- Residue 138
- a UniProt-annotated variant site (in glc3e; formation of protein aggregates)
Similar variants
- TEK p.Asn138fs Pathogenic ★ same residue
- TEK p.Arg1099Ter Pathogenic ★★ same type
- TEK p.Arg849Trp Pathogenic ★★ ⚠ same type
- TEK p.Arg915Cys Pathogenic/Likely pathogenic ★★ same type
- TEK p.Arg915His Pathogenic/Likely pathogenic ★★ same type
- TEK p.Arg918Cys Pathogenic/Likely pathogenic ★★ same type
- TEK p.Gln518Ter Pathogenic/Likely pathogenic ★★ same type
- TEK p.Glu1109Ter Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tek-p-asn138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown